Tree pruning is an important tree management option for reducing shading effects and altering whole-tree water use in smallholder farming systems. In this study, sap flow meters (SFM1s) were used to monitor whole- tree water use in Cordia africana (Cordia), Albizia coriaria (Albizia) and Coffea arabica (coffee) trees in two farms in Eastern Uganda. Overstory trees were subjected to a 50% pruning regime at a 6-month interval over a period of 20 months (July 2018–February 2020). Analysis of variance General Linear Model was performed to assess the influence of tree species, management, season and their interaction on mean daily sap flow. Pairwise Pearson correlation coefficients between daily sap flow and leaf phenology were also obtained. Pruning altered the synchrony in the vegetative phenology of Albizia trees, as leaf cover changes occurred earlier in pruned trees than in unpruned trees. Pruned Cordia and Albizia trees respectively used 22.8% and 50.1% less water than unpruned trees whose average daily water use was 76.5L day1 and 133.7L day1 respectively. Episodes of reverse flows were observed in Albizia trees (pruned and unpruned) and the pruned Cordia during certain periods of the year. There was a statistically significant main effect of tree species, pruning, season and their interaction on daily tree water use (P<0.05). Coffee used 0.1 to 4.3 L of water per day over the 20-month period. While unshaded coffee used more water than shaded coffee, coffee growing under pruned trees used more water than coffee under unpruned trees. This could have resulted from more transpiration pull in coffee resulting from increased radiation with reduced shading. Subsequently, canopy pruning reduced the water demand of the tree component and resulted in recharge in the crop-rooting zone, although this seemed to appear later following consistent pruning. The study findings demonstrate that agroforestry tree canopy pruning can regulate water use in smallholder agroforestry systems, the benefits of other tree products notwithstanding.